# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "doubletrouble" in publications use:'
type: software
license: GPL-3.0-only
title: 'doubletrouble: Identification and classification of duplicated genes'
version: 1.12.0
doi: 10.1093/bioinformatics/btaf043
identifiers:
- type: doi
  value: 10.32614/CRAN.package.doubletrouble
abstract: doubletrouble aims to identify duplicated genes from whole-genome protein
  sequences and classify them based on their modes of duplication. The duplication
  modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal
  duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication
  (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived
  duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler
  classification scheme, duplicates can also be classified into SD- and SSD-derived
  (small-scale duplication) gene pairs. Besides classifying gene pairs, users can
  also classify genes, so that each gene is assigned a unique mode of duplication.
  Users can also calculate substitution rates per substitution site (i.e., Ka and
  Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models
  (GMMs), and classify gene pairs into age groups based on Ks peaks.
authors:
- family-names: Almeida-Silva
  given-names: Fabrício
  email: fabricio_almeidasilva@hotmail.com
  orcid: https://orcid.org/0000-0002-5314-2964
- family-names: Peer
  given-names: Yves
  name-particle: Van de
  email: yves.vandepeer@psb.vib-ugent.be
  orcid: https://orcid.org/0000-0003-4327-3730
preferred-citation:
  type: article
  title: 'doubletrouble: an R/Bioconductor package for the identification, classification,
    and analysis of gene and genome duplications'
  authors:
  - family-names: Almeida-Silva
    given-names: Fabricio
  - family-names: Peer
    given-names: Yves
    name-particle: Van de
    email: yves.vandepeer@psb.vib-ugent.be
    orcid: https://orcid.org/0000-0003-4327-3730
  journal: Bioinformatics
  year: '2025'
  volume: '41'
  issue: '2'
  url: https://academic.oup.com/bioinformatics/article/41/2/btaf043/7979242
  doi: 10.1093/bioinformatics/btaf043
  start: btaf043
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/almeidasilvaf/doubletrouble
commit: 0a45b24aafa7649ea55c4442664a91129d337748
url: https://support.bioconductor.org/t/doubletrouble
date-released: '2024-03-19'
contact:
- family-names: Almeida-Silva
  given-names: Fabrício
  email: fabricio_almeidasilva@hotmail.com
  orcid: https://orcid.org/0000-0002-5314-2964